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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-11-05, 12:56 based on data in:

        General Statistics

        Showing 348/348 rows and 5/6 columns.
        Sample Name% BP Trimmed% Dups% GCLengthM Seqs
        15-033_R1_001
        4.6%
        15-033_R1_001_val_1
        81.2%
        43%
        144 bp
        46.4
        15-033_R2_001
        3.6%
        15-033_R2_001_val_2
        80.6%
        43%
        144 bp
        46.4
        15-091_R1_001
        8.6%
        15-091_R1_001_val_1
        79.1%
        41%
        139 bp
        44.0
        15-091_R2_001
        7.0%
        15-091_R2_001_val_2
        79.5%
        41%
        139 bp
        44.0
        15-092_R1_001
        10.8%
        15-092_R1_001_val_1
        78.9%
        42%
        134 bp
        49.1
        15-092_R2_001
        10.2%
        15-092_R2_001_val_2
        79.5%
        42%
        134 bp
        49.1
        15-152_R1_001
        6.5%
        15-152_R1_001_val_1
        78.4%
        43%
        142 bp
        32.4
        15-152_R2_001
        5.6%
        15-152_R2_001_val_2
        77.3%
        43%
        141 bp
        32.4
        15-154_R1_001
        6.5%
        15-154_R1_001_val_1
        80.2%
        42%
        142 bp
        50.1
        15-154_R2_001
        5.2%
        15-154_R2_001_val_2
        81.0%
        41%
        142 bp
        50.1
        15-161_R1_001
        8.9%
        15-161_R1_001_val_1
        79.1%
        42%
        139 bp
        52.3
        15-161_R2_001
        7.5%
        15-161_R2_001_val_2
        79.8%
        42%
        138 bp
        52.3
        25-046_R1_001
        5.0%
        25-046_R1_001_val_1
        79.4%
        43%
        144 bp
        43.9
        25-046_R2_001
        4.2%
        25-046_R2_001_val_2
        80.4%
        42%
        144 bp
        43.9
        25-047_R1_001
        43.4%
        25-047_R1_001_val_1
        72.4%
        43%
        125 bp
        26.0
        25-047_R2_001
        12.3%
        25-047_R2_001_val_2
        73.3%
        44%
        125 bp
        26.0
        25-048_R1_001
        5.5%
        25-048_R1_001_val_1
        73.8%
        44%
        145 bp
        27.3
        25-048_R2_001
        4.0%
        25-048_R2_001_val_2
        74.4%
        44%
        145 bp
        27.3
        25-049_R1_001
        5.2%
        25-049_R1_001_val_1
        81.0%
        40%
        144 bp
        38.1
        25-049_R2_001
        4.3%
        25-049_R2_001_val_2
        79.6%
        40%
        143 bp
        38.1
        25-050_R1_001
        4.9%
        25-050_R1_001_val_1
        79.0%
        43%
        144 bp
        52.6
        25-050_R2_001
        4.1%
        25-050_R2_001_val_2
        80.0%
        43%
        143 bp
        52.6
        25-051_R1_001
        11.2%
        25-051_R1_001_val_1
        73.7%
        45%
        137 bp
        52.3
        25-051_R2_001
        8.7%
        25-051_R2_001_val_2
        74.8%
        45%
        137 bp
        52.3
        25-052_R1_001
        4.6%
        25-052_R1_001_val_1
        76.5%
        42%
        144 bp
        30.1
        25-052_R2_001
        3.7%
        25-052_R2_001_val_2
        76.2%
        42%
        144 bp
        30.1
        25-053_R1_001
        7.7%
        25-053_R1_001_val_1
        80.4%
        43%
        141 bp
        50.6
        25-053_R2_001
        6.3%
        25-053_R2_001_val_2
        81.2%
        43%
        141 bp
        50.6
        25-054_R1_001
        5.6%
        25-054_R1_001_val_1
        77.8%
        45%
        143 bp
        50.2
        25-054_R2_001
        4.7%
        25-054_R2_001_val_2
        78.7%
        45%
        143 bp
        50.2
        25-055_R1_001
        4.9%
        25-055_R1_001_val_1
        76.2%
        43%
        146 bp
        32.1
        25-055_R2_001
        2.6%
        25-055_R2_001_val_2
        77.6%
        43%
        146 bp
        32.1
        25-056_R1_001
        5.7%
        25-056_R1_001_val_1
        77.8%
        43%
        143 bp
        33.9
        25-056_R2_001
        5.0%
        25-056_R2_001_val_2
        76.8%
        43%
        142 bp
        33.9
        25-058_R1_001
        10.3%
        25-058_R1_001_val_1
        79.1%
        40%
        139 bp
        38.8
        25-058_R2_001
        7.2%
        25-058_R2_001_val_2
        79.7%
        40%
        139 bp
        38.8
        25-059_R1_001
        12.8%
        25-059_R1_001_val_1
        82.2%
        44%
        138 bp
        62.0
        25-059_R2_001
        8.7%
        25-059_R2_001_val_2
        82.6%
        44%
        138 bp
        62.0
        25-060_R1_001
        11.1%
        25-060_R1_001_val_1
        82.1%
        42%
        140 bp
        53.6
        25-060_R2_001
        6.7%
        25-060_R2_001_val_2
        82.7%
        42%
        139 bp
        53.6
        25-109_R1_001
        7.8%
        25-109_R1_001_val_1
        78.4%
        43%
        140 bp
        44.4
        25-109_R2_001
        6.5%
        25-109_R2_001_val_2
        79.5%
        43%
        140 bp
        44.4
        25-110_R1_001
        3.8%
        25-110_R1_001_val_1
        81.7%
        41%
        145 bp
        35.1
        25-110_R2_001
        3.0%
        25-110_R2_001_val_2
        82.4%
        41%
        145 bp
        35.1
        25-112_R1_001
        2.7%
        25-112_R1_001_val_1
        79.8%
        43%
        147 bp
        46.6
        25-112_R2_001
        2.1%
        25-112_R2_001_val_2
        80.2%
        43%
        146 bp
        46.6
        25-113_R1_001
        4.9%
        25-113_R1_001_val_1
        77.0%
        44%
        145 bp
        31.8
        25-113_R2_001
        3.5%
        25-113_R2_001_val_2
        77.5%
        44%
        145 bp
        31.8
        25-114_R1_001
        4.4%
        25-114_R1_001_val_1
        83.5%
        42%
        146 bp
        66.7
        25-114_R2_001
        3.0%
        25-114_R2_001_val_2
        83.4%
        42%
        145 bp
        66.7
        25-115_R1_001
        6.0%
        25-115_R1_001_val_1
        77.0%
        44%
        143 bp
        38.5
        25-115_R2_001
        5.3%
        25-115_R2_001_val_2
        78.1%
        44%
        143 bp
        38.5
        25-116_R1_001
        4.3%
        25-116_R1_001_val_1
        77.0%
        43%
        145 bp
        43.7
        25-116_R2_001
        3.3%
        25-116_R2_001_val_2
        77.9%
        43%
        145 bp
        43.7
        25-117_R1_001
        8.4%
        25-117_R1_001_val_1
        74.7%
        44%
        139 bp
        38.3
        25-117_R2_001
        7.2%
        25-117_R2_001_val_2
        74.6%
        44%
        139 bp
        38.3
        25-119_R1_001
        2.6%
        25-119_R1_001_val_1
        85.1%
        38%
        147 bp
        50.5
        25-119_R2_001
        1.9%
        25-119_R2_001_val_2
        85.1%
        38%
        147 bp
        50.5
        25-120_R1_001
        8.0%
        25-120_R1_001_val_1
        78.6%
        44%
        140 bp
        55.2
        25-120_R2_001
        6.4%
        25-120_R2_001_val_2
        78.5%
        44%
        140 bp
        55.2
        25-167_R1_001
        6.5%
        25-167_R1_001_val_1
        79.5%
        42%
        142 bp
        36.9
        25-167_R2_001
        5.6%
        25-167_R2_001_val_2
        78.2%
        42%
        141 bp
        36.9
        25-168_R1_001
        4.7%
        25-168_R1_001_val_1
        80.1%
        43%
        145 bp
        43.3
        25-168_R2_001
        3.0%
        25-168_R2_001_val_2
        80.2%
        43%
        145 bp
        43.3
        25-169_R1_001
        17.5%
        25-169_R1_001_val_1
        79.3%
        45%
        132 bp
        54.1
        25-169_R2_001
        11.6%
        25-169_R2_001_val_2
        80.2%
        44%
        132 bp
        54.1
        25-170_R1_001
        4.1%
        25-170_R1_001_val_1
        78.3%
        43%
        145 bp
        49.1
        25-170_R2_001
        3.1%
        25-170_R2_001_val_2
        79.0%
        43%
        145 bp
        49.1
        25-171_R1_001
        2.7%
        25-171_R1_001_val_1
        82.4%
        40%
        147 bp
        47.0
        25-171_R2_001
        1.9%
        25-171_R2_001_val_2
        82.6%
        40%
        147 bp
        47.0
        25-172_R1_001
        6.4%
        25-172_R1_001_val_1
        75.1%
        44%
        142 bp
        36.7
        25-172_R2_001
        5.2%
        25-172_R2_001_val_2
        75.9%
        43%
        142 bp
        36.7
        25-174_R1_001
        6.3%
        25-174_R1_001_val_1
        77.6%
        42%
        143 bp
        35.5
        25-174_R2_001
        5.0%
        25-174_R2_001_val_2
        78.5%
        42%
        143 bp
        35.5
        25-175_R1_001
        3.8%
        25-175_R1_001_val_1
        78.7%
        42%
        146 bp
        37.2
        25-175_R2_001
        2.7%
        25-175_R2_001_val_2
        79.0%
        42%
        145 bp
        37.2
        25-177_R1_001
        3.5%
        25-177_R1_001_val_1
        80.6%
        40%
        146 bp
        43.2
        25-177_R2_001
        2.5%
        25-177_R2_001_val_2
        80.6%
        40%
        146 bp
        43.2
        25-179_R1_001
        11.6%
        25-179_R1_001_val_1
        76.8%
        43%
        138 bp
        40.4
        25-179_R2_001
        7.8%
        25-179_R2_001_val_2
        78.0%
        43%
        138 bp
        40.4
        25-180_R1_001
        18.4%
        25-180_R1_001_val_1
        79.2%
        40%
        135 bp
        49.1
        25-180_R2_001
        9.2%
        25-180_R2_001_val_2
        80.0%
        40%
        135 bp
        49.1
        25-185_R1_001
        4.8%
        25-185_R1_001_val_1
        73.3%
        43%
        145 bp
        26.5
        25-185_R2_001
        3.4%
        25-185_R2_001_val_2
        74.1%
        43%
        145 bp
        26.5
        25-186_R1_001
        5.5%
        25-186_R1_001_val_1
        73.1%
        44%
        145 bp
        25.4
        25-186_R2_001
        4.4%
        25-186_R2_001_val_2
        73.8%
        44%
        144 bp
        25.4
        25-193_R1_001
        8.5%
        25-193_R1_001_val_1
        84.6%
        38%
        141 bp
        26.7
        25-193_R2_001
        6.0%
        25-193_R2_001_val_2
        84.3%
        37%
        141 bp
        26.7
        25-194_R1_001
        5.4%
        25-194_R1_001_val_1
        79.9%
        42%
        143 bp
        30.4
        25-194_R2_001
        4.6%
        25-194_R2_001_val_2
        78.6%
        42%
        143 bp
        30.4
        25-195_R1_001
        7.7%
        25-195_R1_001_val_1
        75.5%
        44%
        142 bp
        33.2
        25-195_R2_001
        5.3%
        25-195_R2_001_val_2
        77.3%
        43%
        142 bp
        33.2
        25-202_R1_001
        8.8%
        25-202_R1_001_val_1
        82.4%
        39%
        139 bp
        48.4
        25-202_R2_001
        7.4%
        25-202_R2_001_val_2
        83.0%
        39%
        138 bp
        48.4
        25-203_R1_001
        5.2%
        25-203_R1_001_val_1
        78.7%
        42%
        144 bp
        35.4
        25-203_R2_001
        4.4%
        25-203_R2_001_val_2
        77.4%
        42%
        143 bp
        35.4
        5-002_R1_001
        4.7%
        5-002_R1_001_val_1
        77.7%
        41%
        145 bp
        42.8
        5-002_R2_001
        3.0%
        5-002_R2_001_val_2
        78.7%
        41%
        145 bp
        42.8
        5-003_R1_001
        5.8%
        5-003_R1_001_val_1
        82.1%
        40%
        143 bp
        46.2
        5-003_R2_001
        4.8%
        5-003_R2_001_val_2
        82.6%
        40%
        142 bp
        46.2
        5-004_R1_001
        8.1%
        5-004_R1_001_val_1
        80.5%
        41%
        140 bp
        51.2
        5-004_R2_001
        6.7%
        5-004_R2_001_val_2
        81.4%
        41%
        140 bp
        51.2
        5-005_R1_001
        3.1%
        5-005_R1_001_val_1
        84.6%
        37%
        146 bp
        43.9
        5-005_R2_001
        2.2%
        5-005_R2_001_val_2
        84.8%
        36%
        146 bp
        43.9
        5-006_R1_001
        7.3%
        5-006_R1_001_val_1
        78.0%
        40%
        141 bp
        33.0
        5-006_R2_001
        5.9%
        5-006_R2_001_val_2
        78.0%
        40%
        141 bp
        33.0
        5-007_R1_001
        4.9%
        5-007_R1_001_val_1
        79.7%
        40%
        145 bp
        29.8
        5-007_R2_001
        4.0%
        5-007_R2_001_val_2
        80.3%
        40%
        145 bp
        29.8
        5-008_R1_001
        3.5%
        5-008_R1_001_val_1
        81.2%
        40%
        146 bp
        50.0
        5-008_R2_001
        2.5%
        5-008_R2_001_val_2
        81.5%
        40%
        146 bp
        50.0
        5-009_R1_001
        5.3%
        5-009_R1_001_val_1
        79.3%
        40%
        143 bp
        32.4
        5-009_R2_001
        4.4%
        5-009_R2_001_val_2
        79.5%
        40%
        143 bp
        32.4
        5-010_R1_001
        6.0%
        5-010_R1_001_val_1
        69.6%
        43%
        144 bp
        33.7
        5-010_R2_001
        3.8%
        5-010_R2_001_val_2
        71.7%
        43%
        144 bp
        33.7
        5-012_R1_001
        2.9%
        5-012_R1_001_val_1
        82.3%
        38%
        147 bp
        42.6
        5-012_R2_001
        2.0%
        5-012_R2_001_val_2
        82.2%
        38%
        147 bp
        42.6
        5-014_R1_001
        8.8%
        5-014_R1_001_val_1
        79.9%
        41%
        139 bp
        48.2
        5-014_R2_001
        7.1%
        5-014_R2_001_val_2
        80.6%
        41%
        139 bp
        48.2
        5-015_R1_001
        4.7%
        5-015_R1_001_val_1
        79.6%
        40%
        145 bp
        33.5
        5-015_R2_001
        3.1%
        5-015_R2_001_val_2
        80.7%
        40%
        145 bp
        33.5
        5-061_R1_001
        3.8%
        5-061_R1_001_val_1
        85.0%
        38%
        146 bp
        36.4
        5-061_R2_001
        2.6%
        5-061_R2_001_val_2
        85.0%
        37%
        146 bp
        36.4
        5-063_R1_001
        4.3%
        5-063_R1_001_val_1
        80.9%
        42%
        145 bp
        42.2
        5-063_R2_001
        3.5%
        5-063_R2_001_val_2
        81.4%
        42%
        144 bp
        42.2
        5-066_R1_001
        50.5%
        5-066_R1_001_val_1
        70.0%
        43%
        126 bp
        18.9
        5-066_R2_001
        11.0%
        5-066_R2_001_val_2
        70.6%
        44%
        126 bp
        18.9
        5-067_R1_001
        5.9%
        5-067_R1_001_val_1
        80.2%
        41%
        143 bp
        44.3
        5-067_R2_001
        4.9%
        5-067_R2_001_val_2
        80.5%
        40%
        143 bp
        44.3
        5-069_R1_001
        3.3%
        5-069_R1_001_val_1
        82.9%
        39%
        148 bp
        36.8
        5-069_R2_001
        1.3%
        5-069_R2_001_val_2
        82.7%
        39%
        147 bp
        36.8
        5-071_R1_001
        3.7%
        5-071_R1_001_val_1
        82.7%
        39%
        146 bp
        42.2
        5-071_R2_001
        2.8%
        5-071_R2_001_val_2
        83.0%
        39%
        145 bp
        42.2
        5-073_R1_001
        16.0%
        5-073_R1_001_val_1
        80.1%
        40%
        139 bp
        31.3
        5-073_R2_001
        13.3%
        5-073_R2_001_val_2
        80.5%
        39%
        139 bp
        31.3
        5-074_R1_001
        5.1%
        5-074_R1_001_val_1
        80.1%
        40%
        145 bp
        35.8
        5-074_R2_001
        2.9%
        5-074_R2_001_val_2
        80.8%
        40%
        145 bp
        35.8
        5-075_R1_001
        5.7%
        5-075_R1_001_val_1
        79.0%
        40%
        144 bp
        27.3
        5-075_R2_001
        3.7%
        5-075_R2_001_val_2
        80.4%
        40%
        144 bp
        27.3
        5-121_R1_001
        3.2%
        5-121_R1_001_val_1
        79.5%
        41%
        146 bp
        39.2
        5-121_R2_001
        2.3%
        5-121_R2_001_val_2
        80.1%
        40%
        146 bp
        39.2
        5-122_R1_001
        3.8%
        5-122_R1_001_val_1
        80.9%
        39%
        145 bp
        23.2
        5-122_R2_001
        2.9%
        5-122_R2_001_val_2
        80.7%
        39%
        145 bp
        23.2
        5-123_R1_001
        3.7%
        5-123_R1_001_val_1
        80.6%
        41%
        146 bp
        44.2
        5-123_R2_001
        2.5%
        5-123_R2_001_val_2
        81.2%
        41%
        146 bp
        44.2
        5-124_R1_001
        6.4%
        5-124_R1_001_val_1
        82.9%
        40%
        142 bp
        52.0
        5-124_R2_001
        5.3%
        5-124_R2_001_val_2
        82.8%
        40%
        142 bp
        52.0
        5-125_R1_001
        8.0%
        5-125_R1_001_val_1
        84.2%
        37%
        141 bp
        37.6
        5-125_R2_001
        5.6%
        5-125_R2_001_val_2
        84.8%
        36%
        141 bp
        37.6
        5-126_R1_001
        10.8%
        5-126_R1_001_val_1
        80.6%
        41%
        139 bp
        41.8
        5-126_R2_001
        7.3%
        5-126_R2_001_val_2
        81.4%
        41%
        139 bp
        41.8
        5-127_R1_001
        30.9%
        5-127_R1_001_val_1
        74.4%
        42%
        135 bp
        25.8
        5-127_R2_001
        8.9%
        5-127_R2_001_val_2
        75.5%
        42%
        135 bp
        25.8
        5-128_R1_001
        5.9%
        5-128_R1_001_val_1
        78.4%
        41%
        142 bp
        40.3
        5-128_R2_001
        5.2%
        5-128_R2_001_val_2
        78.4%
        42%
        142 bp
        40.3
        5-130_R1_001
        3.5%
        5-130_R1_001_val_1
        82.8%
        39%
        146 bp
        46.5
        5-130_R2_001
        2.4%
        5-130_R2_001_val_2
        83.4%
        38%
        146 bp
        46.5
        5-131_R1_001
        7.2%
        5-131_R1_001_val_1
        84.7%
        39%
        141 bp
        51.1
        5-131_R2_001
        6.1%
        5-131_R2_001_val_2
        84.0%
        39%
        140 bp
        51.1
        5-133_R1_001
        5.5%
        5-133_R1_001_val_1
        77.9%
        41%
        144 bp
        30.5
        5-133_R2_001
        3.9%
        5-133_R2_001_val_2
        79.0%
        41%
        144 bp
        30.5
        5-135_R1_001
        7.8%
        5-135_R1_001_val_1
        76.6%
        40%
        141 bp
        17.7
        5-135_R2_001
        6.4%
        5-135_R2_001_val_2
        76.8%
        39%
        140 bp
        17.7
        5-181_R1_001
        4.2%
        5-181_R1_001_val_1
        85.6%
        39%
        145 bp
        59.3
        5-181_R2_001
        3.4%
        5-181_R2_001_val_2
        85.7%
        38%
        145 bp
        59.3
        5-182_R1_001
        3.8%
        5-182_R1_001_val_1
        77.7%
        42%
        146 bp
        34.8
        5-182_R2_001
        2.9%
        5-182_R2_001_val_2
        78.7%
        42%
        146 bp
        34.8
        5-187_R1_001
        5.9%
        5-187_R1_001_val_1
        81.4%
        41%
        142 bp
        71.2
        5-187_R2_001
        5.0%
        5-187_R2_001_val_2
        81.7%
        40%
        142 bp
        71.2
        5-188_R1_001
        5.3%
        5-188_R1_001_val_1
        78.1%
        41%
        143 bp
        36.7
        5-188_R2_001
        4.5%
        5-188_R2_001_val_2
        78.0%
        41%
        143 bp
        36.7
        5-189_R1_001
        3.5%
        5-189_R1_001_val_1
        78.8%
        41%
        147 bp
        31.3
        5-189_R2_001
        2.5%
        5-189_R2_001_val_2
        79.3%
        41%
        147 bp
        31.3
        5-197_R1_001
        7.5%
        5-197_R1_001_val_1
        79.0%
        44%
        142 bp
        53.7
        5-197_R2_001
        5.9%
        5-197_R2_001_val_2
        79.8%
        44%
        142 bp
        53.7

        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.11 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.